The department offers the Doctor of Philosophy in Operations Research degree. The program begins with advanced course work guided by the student's doctoral committee and leading to qualifying examinations in optimization, statistics, and stochastic processes as well as completion of a minor field of study outside of operations research. The primary emphasis then shifts to the student's research program, culminating in the Ph.D. dissertation.

An applicant to the Ph.D. program who is not already a student at NPS should submit transcripts of previous academic and professional work, plus results of a current Graduate Record Examination (GRE) general test, to the Director of Admissions, Code 01C3, Naval Postgraduate School, Monterey, CA 93943-5100. Detailed admission procedures may vary depending on the individual's location and position. However, in all cases, the student must fulfill the general school requirements for the doctoral degree. Residency for this program generally requires three years beyond completion of a master's degree.